I think this scene is ironic only if you think about what he is saying in a particular way. If you think he is scolding them for being savage to one another, then it is ironic.

The irony here would be that the naval officer is scolding the boys because they have ended up fighting and killing one another. It is ironic for a military officer to be saying this. With Britain at war, he has presumably caused the death of many people. He and the other adults of Britain have not put on a "good show" themselves and so it is ironic for him to criticize the boys for what they have done.

If, however, you think he is criticizing them for not looking neater and cleaner and for not having an acknowledged leader, this is not nearly so ironic. He does symbolize this sort of order and so he could be expected to criticize them for that.